The Proteomics Core Facility began operation in 1998 and was one of the first laboratories in the nation equipped for high throughput proteomic analysis based on laboratory automation. It is directed by Dr. Jon Klein, who is also a member of the Internal Advisory Board of the MT-COBRE. He is assisted by two laboratory personnel who have had several years experience in this area. Dr. Klein is available to all MT-COBRE investigators on a collaborative or consultative basis. The excellence of this laboratory is attested by the fact that it is used as a 'beta testing' site for a number of companies making proteomics-associated products. The Core Proteomics Laboratory is uniquely equipped with robotic workstations that increase gel throughput, image analysis, spot excision, in-gel peptide digestion, and MALDI-MS sample preparation. The automated workstations include a Propic gel spot picker that visualizes and excises spots from fluorescence-stained gels and a ProGest station that automates in-gel trypsin digestion in a 96 or 384 well format. The laboratory also contains a ProMS robot that automates the desalting, concentrating and spotting of peptide samples onto MALDI targets (Genomics Solutions, Inc.) thereby allowing fully integrated high-throughput analysis of protein samples. MALDI-MS analysis is performed using a Micromass, Inc. TOF-Spec 2E. Recently, the laboratory instituted automated analysis of high-resolution two-dimensional gels using Progenesis software from Nonlinear Dynamics, Inc. The Progenesis software significantly decreases analysis time of two-dimensional gels, thereby accelerating throughput. The Proteomics Core Facility will play an important role in several of the MT-COBRE projects, particularly in looking at downstream effects of target inhibition.